Background: This study tries to determine the prevalence and co-morbidities associated with hypomineralised second primary molars (HSPM) in 8- to 10- year-old children in Ile-Ife, Nigeria; and the co-existence of HSPM and Molar Incisor Hypomineralisation (MIH) in the study population. Methods: This was a cross sectional study involving 8- to 10- year-old children in schooling in suburban Nigeria. Information was collected on the child's age, sex and socioeconomic status. Intraoral examination was conducted to determine the presence of HSPM, MIH, caries and the oral hygiene status of study participants. The severity of HSPM was also determined. The prevalence of HSPM, the association between HSPM, sex and socioeconomic status of study participants, the difference in the prevalence of caries and poor oral hygiene in children with and without HSPM, and the prevalence of HSPM and MIH co-morbidity were determined. Results: Twenty seven of the 469 children examined (5.8 %) had HSPM. The tooth prevalence of HSPM was 3.9 %. There was no significant sex (p = 0.06), age (p = 0.41), and socioeconomic status (p = 0.67) differences between children with HSPM and without HSPM. More children with HSPM had caries (p â‰¤ 0.001) and poor oral hygiene (p = 0.01). Children with HSPM have increased odds having dental caries (AOR: 6.34; CI: 2.78â€“14.46; p = <0.001) and reduced odds of having good oral hygiene (AOR: 0.32; CI: 0.13â€“0.78; p = 0.01) when compare with children without HSPM. Also 77.8 % of children with HSPM also had MIH. Conclusion: The prevalence of HSPM in the study population is significantly high. The large number of children with HSPM and MIH also suggests that HSPM is a predisposing factor for MIH. The significantly higher proportion of children with HSPM who had caries and poor oral hygiene makes it imperative to institute screening programmes for HSPM/MIH in the study population.