Gilbert’s syndrome (GS) is a benign hereditary disorder of bilirubin conjugation resulting in an isolated, elevated blood level of unconjugated bilirubin. An individual with GS is typically asymptomatic and does not require treatment. Thrombocytopenia is not a known feature of GS and may suggest an alternate or co-existing pathology. We report a rare case of a 40-year-old male, with an incidental finding of mildly increased unconjugated bilirubin levels on two different occasions with moderate thrombocytopenia in the absence of any aggravating factors. Further investigations were done to rule out autoimmune, infectious or hemolytic causes. This report underscores the need to consider genetic disorders in the differential diagnosis of patients with unexplained thrombocytopenia, it also highlights the critical value of laboratory findings in avoiding misdiagnosis of GS.