The objectives of the present study were to describe for first time the prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type-2 (PCV2) among pig farms in Greece and the association between risk factors and PRRSV, PCV2 PCR-status. PRRSV and PCV2 are the leading causes of huge financial losses in swine industry worldwide. Despite the implementation of control measures, both remain a major problem for the majority of pig farms. Identification of risk factors, which can lead to PRRSV and/or PCV2 infection, could be useful in preventing it. The study included 59 pig farms, across Greece, with a total population of 22.500 sows, which represent about 40% of the entire sow capacity of Greek swine production. Data regarding herd health management protocols were collected from each farm. Additionally, blood samples from breeding stock, weaners, growers and finishers were taken from each farm. The sera were tested for PRRSV and PCV2, the results indicated that both viruses remain a major challenge for the Greek swine industry. Finally, main risk factors involved in the infection process by these viruses were identified and could be used for future monitoring both diseases. In particular, vaccination programs such as the mass PRRSV vaccination with modified-live virus (MLV) in breeding stock during the last stages of gestation or with killed-virus (KV) during the middle of gestation are more likely to be associated with PRRSV seropositivity. Farms with low biosecurity level are associated with higher PRRSV circulation. It has, also, been revealed that breeding stock is more likely to be associated with PCV2 active circulation compared to weaners and growers. In conclusion, our results could be the basis of the development of surveillance protocols for a national monitoring system for PRRSV and PCV2, which could prevent future infection of Greek farms.