How do I detect that an iOS app is running on a jailbroken phone?

It depends what you mean by jailbreak. In the simple case, you should be able to see if Cydia is installed and go by that - something like

NSString *filePath = @"/Applications/Cydia.app";if ([[NSFileManager defaultManager] fileExistsAtPath:filePath]){   // do something useful}

For hacked kernels, it's a little (lot) more involved.

This is a code that combine some answers I found for this need, and will give you much higher success rate :

BOOL isJailbroken(){#if !(TARGET_IPHONE_SIMULATOR)   if ([[NSFileManager defaultManager] fileExistsAtPath:@"/Applications/Cydia.app"] ||       [[NSFileManager defaultManager] fileExistsAtPath:@"/Library/MobileSubstrate/MobileSubstrate.dylib"] ||       [[NSFileManager defaultManager] fileExistsAtPath:@"/bin/bash"] ||       [[NSFileManager defaultManager] fileExistsAtPath:@"/usr/sbin/sshd"] ||       [[NSFileManager defaultManager] fileExistsAtPath:@"/etc/apt"] ||       [[NSFileManager defaultManager] fileExistsAtPath:@"/private/var/lib/apt/"] ||       [[UIApplication sharedApplication] canOpenURL:[NSURL URLWithString:@"cydia://package/com.example.package"]])  {         return YES;   }   FILE *f = NULL ;   if ((f = fopen("/bin/bash", "r")) ||      (f = fopen("/Applications/Cydia.app", "r")) ||      (f = fopen("/Library/MobileSubstrate/MobileSubstrate.dylib", "r")) ||      (f = fopen("/usr/sbin/sshd", "r")) ||      (f = fopen("/etc/apt", "r")))  {         fclose(f);         return YES;   }   fclose(f);   NSError *error;   NSString *stringToBeWritten = @"This is a test.";   [stringToBeWritten writeToFile:@"/private/jailbreak.txt" atomically:YES encoding:NSUTF8StringEncoding error:&error];   [[NSFileManager defaultManager] removeItemAtPath:@"/private/jailbreak.txt" error:nil];   if(error == nil)   {      return YES;   }#endif   return NO;}

+(BOOL)isJailbroken {    NSURL* url = [NSURL URLWithString:@"cydia://package/com.example.package"];    return [[UIApplication sharedApplication] canOpenURL:url];}

Checking the file path /Applications/Cydia.app is not allowed on a normal phone? I've never heard of Apple detecting this and rejecting an app for it, but Apple is unpredictable. Cydia has a URL scheme cydia:// which can be legally checked with UIApplication canOpenURL: