This study aimed to describe the microbiological characteristics of acute septic arthritis (SA) and osteomyelitis (OM) in children. Cases of children (0–15 years) with SA/OM were identified through a retrospective search of hospital discharge codes over a six-year period. In addition, a systematic literature search and meta-analysis of studies reporting culture results of children with SA/OM was performed. In our retrospective chart review, we identified 65 cases of OM and 46 cases of SA. The most frequently cultured organisms in both conditions were Gram-positive cocci, primarily Staphylococcus aureus. On admission, most patients had a normal white blood cell count (WCC) but elevated C-reactive protein (CRP) and/or erythrocyte sedimentation rate (ESR). Bacteraemia was associated with a longer mean length of hospitalization for both infections. Considering our results and the meta-analysis, we found low rates of culture-positivity in cases of clinically confirmed infection. In SA, articular fluid was culture-positive in 42.49 % [95 % confidence interval (CI) 28.39–57.23]. In OM, intra-operative samples were culture-positive in 52.65 % (95 % CI 30.54–74.22). Bacteraemia was detected in 23.91 % (95 % CI 8.40–44.24) of children with SA and 21.48 % (95 % CI 10.89–34.47) with OM. Despite appropriate sampling, a positive microbiological diagnosis is often lacking in paediatric acute osteoarticular infection using standard culture-based methods. This highlights the need for validation and use of more sensitive diagnostic methods, such as PCR.