Enchondromas (ECs) and atypical cartilaginous tumours (ACTs), respectively, represent benign and intermediate cartilaginous bone tumours. Differentiation between these tumour entities bears difficulties, as histology and MRI cannot always provide exact diagnoses. Observation of the natural course of ECs/ACTs via follow-up MRIs might support tumour distinction without needing biopsy harbouring sampling error. Reports of patients that had undergone MRI exams of the knee (n = 44.762) or shoulder (n = 21.550) at a single radiology institute between 01.01.2007 and 01.03.2020 were searched for ECs/ACTs with at least one follow-up MRI. Scans of 176 patients (with 182 cartilage lesions) fulfilling these criteria were subsequently re-examined together with corresponding MRI reports to evaluate morphological tumour development over time, focusing on potential alterations of lesion size, tumour-related oedema, and scalloping. Median follow-up time was 27 ± 53 months for knee tumours and 26 ± 32 months for shoulder lesions. Presence of tumour growth was significantly higher in ACTs than in ECs both at the knee (p = 0.04) and shoulder (p = 0.03). While ACTs were associated with median tumour growth rates of 0.039 mm/month (knee) and 0.083 mm/month (shoulder), ECs of the knee and shoulder showed lower median growth rates equivalent to 0.0 mm/month (p < 0.01, p < 0.01). ECs and ACTs both presented stable regarding tumour-related oedema and scalloping during follow-up. ACTs and ECs show different tumour growth rates. Growth rates are slow for both, ECs and ACTs, supporting the current concept of watchful waiting. ECs may decrease in size. Follow-up MRIs may support the radiological differentiation of cartilage lesions. Question Both singular MRI and histological examination have limitations regarding differentiation of enchondromas (EC) and atypical cartilaginous tumours (ACTs). Findings Median ACT growth rates were 0.039 mm/month (knee) and 0.083 mm/month (shoulder), while median growth rates of EC in the knee and shoulder were 0.0 mm/month. Clinical relevance Active surveillance is a safe strategy when dealing with ECs and ACTs of the long bones; follow-up MRIs may support tumour distinction of cartilage lesions, as ECs and ACTs show different growth behaviour.