Objective: Analyzing the association between Metabolic Syndrome (MS) risk factors and work absenteeism due to illnesses among University Hospital employees in Salvador City, Bahia, Brazil. Methods: Cross-sectional study comprised 1173 Bahia Federal University Hospital employees: 57.3% of them were federal employees (statutory officers) and 42.7% were civil servants (CLT employees). Participants were in the age group 41.5 years: 69.4% were female and 30.6% were male. Results: MS prevalence in employees reached 6.6%; women accounted for 69.7% of the total. The percentage increases with age and has similar proportion among direct-care providers and ancillary supports personnel, 40.8% and 39.5%, respectively. The risk factor analysis showed 25% hypertension, 54.6% weight excess (18.4% obese and 36.2% overweight patients), 20% hypercholesterolemia, 9.9% hypertriglyceridemia and 6.5% diabetes mellitus prevalence. Absenteeism longer than one day within the studied population reached 40.1%. Osteoarticular diseases were the most common reason for absenteeism, accounting for 50.7% of it: 62.6% of whom were either overweight or obese. The mean cost with absenteeism per employee was R$5492.87 ($2347.00 US Dollars), and it corresponds to annual cost of R 2,587,139.53 ($1,105,610.00 US Dollars). The highest cost with absenteeism caused by illnesses was recorded for female workers; for federal employees who were patient caregivers, who worked in the Pediatric Centre and who worked at night shifts. Conclusion: The high Metabolic Syndrome risk factors and overweight incidence are responsible for the increased costs faced by hospitals due to high absenteeism rates.