To protect the virus in the specimen from stressors in the environment which can lead to loss of biological properties and ultimately affect the isolation, there is need to use good quality and appropriate transport system to maintain the virus. Certain virus transport media have proven to be effective and convenient for isolation of swine influenza virus using different culture system. This study was designed to know which of the transport medium: Phosphate Buffer Saline-Glycerol Based or Dulbecco’s Modified Eagle Medium (D-MEM) will be sensitive for the isolation of swine influenza virus using 10 – 12 days old fertile embryonated hen’s egg and Mardin Darby Canine Kidney (MDCK) as the culture systems. A total of 186 nasal swabs were collected from 93 pigs from August to September, 2010 using both PBS-Glycerol and D-MEM as transport medium. Isolation of influenza virus was carried out using conventional cell culture (MDCK) and 10-12day old embryonated hen’s eggs. Isolates were identified by Haemagglutination-Inhibition (HAI) test using World Health Organization (WHO) influenza virus reference antisera. PBS-Glycerol Based Transport Medium yielded 15(16.1%) influenza isolates while D-MEM yielded1 (1.1%) using the two culture systems. PBS-Glycerol Based Transport Medium yielded more isolates which is in line with the fact that a good viral transport medium should allow for survival and diagnosis of viral infections.