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This study aimed to determine the prevalence of problem behaviors in adults with intellectual disabilities and to investigate which factors are independently associated with problem behaviors. A population-based cohort (n = 1023) had comprehensive individual assessments. Data were examined using multivariate logistic regression. The prevalence of problem behaviors was 22.5% (psychiatrists’ opinion) or 18.7% (DC-LD criteria). Factors independently associated with problem behaviors were lower ability level, female gender, living in a congregate care setting or with paid carer support (rather than living with a family carer), having urinary incontinence; visual impairment, not having Down syndrome, and not having severe physical disabilities. Further studies focusing on the etiology, course, and treatment of problem behaviors are required.