Background: Absenteeism in the health sector is frequently referred to as the loss of scheduled time due to unscheduled work absence which has remained a long-standing challenge worldwide. Approval for the leave should be obtained from Heads of the institution before the leave with acting duty. However, being absent from work without prior information has been a major issue among health assistants in hospitals. This study was aimed at analyzing the absenteeism among health assistants in Base Hospitals in the Batticaloa district. Materials and methods: Descriptive cross-sectional study was carried out in all four Base Hospitals (BHs) in Batticaloa District. Data collection was carried out in May 2019 by self-administered questionnaire. Results: One hundred and fourteen (49.1%) out of 232 HA had at least one spell of absence in the year 2018. Among the four BHs in the Batticaloa district, BH Eravur showed the highest and BH Kaluwanchikudy showed the lowest absentee percentage with statistical significance (P<0.01). The overall absenteeism rate was 2.3% with BH Eravur having the highest (4.25%) and BH Kaluwanchikudy having the lowest (0.95%) absenteeism rate. Respondents whose jobs were stressful were more likely to be absent from work compared with their counterparts (OR = 4.13). Nearly 45% of absentees had stated that the reason for absence was sickness. Conclusion: This study concluded that findings showed that up to half of the study subjects experienced at least one spell of absence. Also, it is significantly different between individual institutions. Even though overall absenteeism rate was low it differs significantly among hospitals.