Cases of exertional heat stroke have been reported every year during basic training for Royal Thai Army (RTA) conscripts. Prevention is an important strategy to reduce the incidence of heat-related illnesses. We conducted a study to identify potential indicators for the prevention and monitoring of heat-related illnesses among military conscripts undergoing basic training in Thailand. All newly inducted RTA conscripts in 5 basic training units in 5 regions in Thailand were invited to participate in a prospective cohort study from May 1 to July 9, 2013. The incidence rate of heat-related illnesses and the incidence rate ratio (IRR) based on a Poisson regression model were used to identify the independent factors associated with heat-related illnesses, daily tympanic (body) temperatures higher than 37.5°C, >3% decreases in body weight in one day, and the production of dark brown urine. Eight hundred and nine men aged 21.4 (±1.13) years were enrolled in this study. The prevalence of a body mass index (BMI) ≥30 kg/m2 was 5.5%. During the study period, 53 subjects (6.6%) representing 3.41/100 person-months (95% confidence interval (CI), 2.55-4.23) developed heat-related illnesses (excluding heat rash), and no subjects experienced heat stroke. The incidence rates of a daily tympanic temperature >37.5°C at least once, body weight loss of >3% per day, and the production of dark brown urine at least once were 8.27/100 person-months (95% CI, 7.69-8.93), 47.91/100 person-months (95% CI, 44.22-51.58), and 682.11/100 person-months (95% CI, 635.49-728.52), respectively. The sole identified independent factor related to the incidence of heat-related illnesses was a BMI ≥30 kg/m2 (adjusted IRR = 2.66, 95% CI, 1.01-7.03). In conclusion, a high BMI was associated with heat-related illnesses among conscripts undergoing basic training in Thailand. Daily monitoring of heat-related illnesses, body temperature, body weight and urine color in each new conscript during basic military training was feasible.