Early mortality syndrome (EMS) refers to acute mortality within approximately 35 days of shrimp culture. It is often equated with acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio isolates that produce Pir-like toxins. To better understand EMS, 200 Thai shrimp ponds were randomly selected prior to stocking and subsequently sampled from 19/08/2013 to 23/04/2014 to determine the pond prevalence of various pathologies, and particularly those targeting the shrimp hepatopancreas (HP). Ponds exhibiting acute mortality within 35 days were labeled EMS ponds while others were labeled non-EMS ponds. Shrimp samples from each pond (10) were subjected to histological analysis focused on hepatopancreatic (HP) lesions. Similar samples (10) were tested by PCR for the microsporidian Enterocytozoon hepatopenaei (EHP), white spot syndrome virus (WSSV), yellow head virus (YHV) and Vibrio that cause AHPND. Preservation failed for 4 ponds. Results from the 196 ponds remaining were divided, into 4 groups based largely on HP histology: (1) ponds positive for AHPND by histology and/or PCR at 20.9% prevalence (41/196); (2) ponds showing HP bacterial lesions at 14.8% prevalence (29/196); (3) ponds showing collapsed HP tubule epithelia at 25.0% prevalence (49/196); and (4) ponds showing no HP pathology (normal HP) at 39.3% prevalence (77/196) ponds. The overall prevalence of EMS ponds (i.e., mortality ≤35 days) was 16.3% (32/196), but only 18/32 (56.3%) of these fell within AHPND Group 1. The other 14 EMS ponds (43.7%) were divided among the remaining three groups: Group 2 with HP bacterial lesions (3/32 = 9.4%), Group 3 with collapsed HP tubule epithelia (1/32 = 3.1%) and Group 4 with normal HP histology (a surprising 10/32 = 31.2%). Across all groups, prevalence of ponds exhibiting aggregated transformed microvilli (ATM) was high at 79.8%, as was prevalence of EHP at 60.7%. The overall prevalence of WSSV was low at 4.1% (8/196), while YHV was not found. Overall, the results indicated that equating EMS with AHPND without confirmatory analysis could lead to overestimation of its impact on shrimp aquaculture and to failure in recognizing other important causes of early mortality. •Determination of shrimp pathogens and pathologies were carried out in the 200 pre-selected Thai shrimp ponds.•Among 196 ponds examined, 32 ponds were reported to be EMS ponds.•Only 18 in 32 EMS ponds were found to be positive for AHPND by histology and/or PCR.•Shrimp EMS is not equal to AHPND.