diff --git a/src/common.cpp b/src/common.cpp
index 6ec9cdb..54a83ff 100644
--- a/src/common.cpp
+++ b/src/common.cpp
@@ -1 +1,40 @@
-#include "common.h"
\ No newline at end of file
+#include "common.h"
+
+void writeEscapedJsonString(std::ostream& output, const std::string& input) {
+	for(size_t i = 0; i < input.size(); i++) {
+		const unsigned char c = static_cast<unsigned char>(input[i]);
+		switch(c) {
+			case '"':
+				output << "\\\"";
+				break;
+			case '\\':
+				output << "\\\\";
+				break;
+			case '\b':
+				output << "\\b";
+				break;
+			case '\f':
+				output << "\\f";
+				break;
+			case '\n':
+				output << "\\n";
+				break;
+			case '\r':
+				output << "\\r";
+				break;
+			case '\t':
+				output << "\\t";
+				break;
+			default:
+				if(c < 0x20) {
+					const char* hex = "0123456789abcdef";
+					output << "\\u00";
+					output << hex[(c >> 4) & 0x0F];
+					output << hex[c & 0x0F];
+				} else {
+					output << static_cast<char>(c);
+				}
+				break;
+		}
+	}
+}
\ No newline at end of file
diff --git a/src/common.h b/src/common.h
index 911888b..ed9c3bf 100644
--- a/src/common.h
+++ b/src/common.h
@@ -1,6 +1,9 @@
 #ifndef COMMON_H
 #define COMMON_H
 
+#include <ostream>
+#include <string>
+
 #define FUSIONSCAN_VER "0.8.0"
 
 #define _DEBUG true
@@ -42,5 +45,6 @@ static const int PACK_IN_MEM_LIMIT = 100;
 static const int DUPE_NORMAL_LEVEL = -1;
 static const int DUPE_HIGH_LEVEL = -2;
 
+void writeEscapedJsonString(std::ostream& output, const std::string& input);
 
 #endif /* COMMON_H */
diff --git a/src/jsonreporter.cpp b/src/jsonreporter.cpp
index 35b7ad3..9d2ead0 100644
--- a/src/jsonreporter.cpp
+++ b/src/jsonreporter.cpp
@@ -19,9 +19,13 @@ extern string command;
 
 void JsonReporter::run() {
     mFile << "{" << endl;
-    mFile << "\t\"command\":\"" << command << "\"," << endl;
+    mFile << "\t\"command\":\"";
+    writeEscapedJsonString(mFile, command);
+    mFile << "\"," << endl;
     mFile << "\t\"version\":\"" << FUSIONSCAN_VER << "\"," << endl;
-    mFile << "\t\"time\":\"" << getCurrentSystemTime() << "\"," << endl;
+    mFile << "\t\"time\":\"";
+    writeEscapedJsonString(mFile, getCurrentSystemTime());
+    mFile << "\"," << endl;
     mFile << "\t\"fusions\":{";
 
     bool isFirstMut = true;
@@ -42,25 +46,47 @@ void JsonReporter::run() {
         else
             mFile << "," << endl;
 
-        mFile << "\t\t\"" <<  fusion.mTitle << "\":{" << endl;
+        mFile << "\t\t\"";
+        writeEscapedJsonString(mFile, fusion.mTitle);
+        mFile << "\":{" << endl;
             mFile << "\t\t\t\"" <<  "left" << "\":{" << endl;
-                mFile << "\t\t\t\t\"" <<  "gene_name" << "\":" << "\"" << fusion.mLeftGene.mName << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":" << "\"" << fusion.mLeftGene.mChr << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "gene_name" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mLeftGene.mName);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mLeftGene.mChr);
+                mFile << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "position" << "\":" <<  fusion.mLeftGene.genePos2ChrPos(fusion.mLeftGP.position) << "," << endl;
-                mFile << "\t\t\t\t\"" <<  "reference" << "\":" << "\"" << fusion.mLeftRef << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":" << "\"" << fusion.mLeftRefExt << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "pos_str" << "\":" << "\"" << fusion.mLeftPos << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "reference" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mLeftRef);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mLeftRefExt);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "pos_str" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mLeftPos);
+                mFile << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "exon_or_intron" << "\":" << "\"" << (fusion.mLeftIsExon?"exon":"intron") << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "exon_or_intron_id" << "\":" << fusion.mLeftExonOrIntronID << "," << endl;
                 mFile << "\t\t\t\t\"" <<  "strand" << "\":" << "\"" << (fusion.isLeftProteinForward()?"forward":"reversed") << "\"" << endl;
             mFile << "\t\t\t}, " << endl;
             mFile << "\t\t\t\"" <<  "right" << "\":{" << endl;
-                mFile << "\t\t\t\t\"" <<  "gene_name" << "\":" << "\"" << fusion.mRightGene.mName << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":" << "\"" << fusion.mRightGene.mChr << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "gene_name" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mRightGene.mName);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "gene_chr" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mRightGene.mChr);
+                mFile << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "position" << "\":" << fusion.mRightGene.genePos2ChrPos(fusion.mRightGP.position) << "," << endl;
-                mFile << "\t\t\t\t\"" <<  "reference" << "\":" << "\"" << fusion.mRightRef << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":" << "\"" << fusion.mRightRefExt << "\"," << endl;
-                mFile << "\t\t\t\t\"" <<  "pos_str" << "\":" << "\"" << fusion.mRightPos << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "reference" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mRightRef);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "ref_ext" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mRightRefExt);
+                mFile << "\"," << endl;
+                mFile << "\t\t\t\t\"" <<  "pos_str" << "\":\"";
+                writeEscapedJsonString(mFile, fusion.mRightPos);
+                mFile << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "exon_or_intron" << "\":" << "\"" << (fusion.mRightIsExon?"exon":"intron") << "\"," << endl;
                 mFile << "\t\t\t\t\"" <<  "exon_or_intron_id" << "\":" << fusion.mRightExonOrIntronID << "," << endl;
                 mFile << "\t\t\t\t\"" <<  "strand" << "\":" << "\"" << (fusion.isRightProteinForward()?"forward":"reversed") << "\"" << endl;
diff --git a/src/match.cpp b/src/match.cpp
index 1f81a6d..0d40757 100644
--- a/src/match.cpp
+++ b/src/match.cpp
@@ -89,6 +89,10 @@ int Match::countUnique(vector<Match*>& matches) {
 }
 
 void Match::printReadToJson(ofstream& file, string pad) {
-    file << pad << "\"seq\":" << "\"" <<  mRead->mSeq.mStr << "\"," << endl;
-    file << pad << "\"qual\":" << "\"" <<  mRead->mQuality << "\"" << endl;
+    file << pad << "\"seq\":\"";
+    writeEscapedJsonString(file, mRead->mSeq.mStr);
+    file << "\"," << endl;
+    file << pad << "\"qual\":\"";
+    writeEscapedJsonString(file, mRead->mQuality);
+    file << "\"" << endl;
 }