In Mekong Delta, viral infection, including white spot syndrome virus (WSSV), monodon baculovirus (MBV), heptopancreatic parvovirus (HPV), infectious hypodermal and hematopoietic necrosis virus (IHHNV) and gill-associated nidovirus (GAV) frequently infect cultured shrimp starting at the postlarvae stage. These viral infections cause high mortality of shrimp and affect the farmer’s income. Previous studies mainly focused on the detection, transmission and genetic variation of the pathogens, but few studied the correlation between disease occurrence and other factors, including pond conditions, culture technique and management. Three studies analysed the association of culture factors with the WSSV disease incidence determining risk and potential protective factors in freshwater rice-shrimp systems, and brackish water polyculture and monoculture of black tiger shrimp (Penaeus monodon). Studies on the risk and protective factors in the odd of viral diseases in rice-shrimp rotation were lacking, while in 2011 the Early Mortality Syndrome (EMS)/Acute Hepatopancreatic Necrosis Syndrome (AHPNS) caused the great losses of cultured shrimp in Mekong Delta. This study was carried out to describe the culture status of shrimp in Mekong Delta and to identify the risk and/or protective factors that related to disease incidences in black tiger shrimp cultured in 2011. Through interviews, 58 variables collected from 191 farmers (64: rice-shrimp rotation and 127: intensive system) in Soc Trang and Bac Lieu Provinces, Viet Nam. The data were analysed in two steps of variable reduction to increase model stability and binary logistic regression to identify the risk and/or protective factors. The results showed that the risk factors were pond size (entire dataset, rice-shrimp rotation and intensive culture), settling pond (entire dataset), period of pond dry (entire dataset), stocking density first (rice-shrimp rotation), and stocking density second (rice-shrimp rotation). The potential protective factors were the mode of water intake (entire dataset), water level (entire dataset and rice-shrimp rotation), water quality parameters before stocking (entire dataset), and fry test (rice-shrimp rotation)