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Background Background incidence rates (IRs) of potential safety outcomes among vaccine eligible individuals can inform assessment of vaccine safety. Vaccine safety surveillance often uses claims databases, but the impact of outcome definitions on background IR estimates is largely unexplored. Using two definitions for each outcome, we estimated background IRs of 32 cardiac, metabolic, allergic, autoimmune, neurologic, hematologic and nephrologic outcomes among individuals eligible to receive pneumococcal vaccination. Methods We defined a cohort of individuals aged 6–100 years in US commercial health plans who had ≥12 months of health plan enrollment between January 2007 and August 2014 and no previous record of conjugate or simple polysaccharide pneumococcal vaccination. We developed a sensitive and a specific definition for each outcome, with the specific definition requiring evidence of additional care consistent with the outcome. IRs per 100,000 person-years for each outcome were presented overall and stratified by age, gender, and invasive pneumococcal disease (IPD) risk category. Results We followed 19.9 million individuals for a median of 2.5 years. Wide variation was seen in IRs across different definitions of the 32 outcomes, with 19 (59%) outcomes having a specific definition IR less than half of the sensitive definition IR. IRs were particularly variable by definition for outcomes categorized as either hematologic/nephrologic or neurologic (mean ratio of specific IR to sensitive IR = 0.26 and 0.30, respectively). Across definitions, the IRs of the 32 outcomes were often highest in females, adults ≥65, and those at higher IPD risk. Conclusions Background IRs of safety outcomes relevant to populations indicated for pneumococcal vaccine varied by outcome definitions and population subgroups in this large US commercially-insured population. Given large differences in estimated IRs using sensitive versus specific case definitions, neurologic, and hematologic/nephrologic safety outcomes as compared to allergic and autoimmune outcomes may warrant more refined definitions and medical record validation.