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There is a lack of knowledge on the registration of body mass index (BMI) and prevalence of obesity-related complications in the Belgian healthcare system. We therefore evaluated these in Belgians living with overweight or obesity. BMI registration and obesity-related complication prevalences were determined using cross-sectional data from a Belgian general practitioners' morbidity registry (Intego) with 208 891 personal records and from 3605 visitors to an obesity clinic. Two Intego data subsets were used: 53 555 individuals with and 84 017 individuals without registered BMI. Groups were compared using chi-square tests (p-value of < 0.05). For Intego data, BMI was registered in 25.6% of cases. Individuals with registered BMI (mean BMI 27.1 ± 5.5 kg/m²) had a higher prevalence of hypertension (30.1% vs. 17.0%), dyslipidemia (26.9% vs. 14.7%), prediabetes (17.0% vs. 7.9%), type 2 diabetes (12.7% vs. 4.4%) and sleep apnea (3.8% vs. 1.5%) compared to people without registered BMI. People assessed at the obesity clinic (mean BMI 39.0 ± 6.5 kg/m²) had higher prevalences of hypertension (43.1% vs. 37.5%), dyslipidemia (44.4% vs. 32.9%) and sleep apnea (37.9% vs. 5.5%) compared to Intego individuals with BMI ≥ 25 kg/m²(mean BMI 30.3 ± 4.3 kg/m²). BMI is registered only in 25% of patient files in general practice, and people with a registered BMI in general practice have a substantially higher prevalence of the five obesity-related complications than people without registered BMI. When registered, mean BMI is substantially lower than in the obesity clinic, but the prevalence of complications is already substantial, though lower than in the obesity clinic.