Background Conflict in Nigeria displaced millions of people, and some settled in camp-like locations within the country. Evidence on the association between living conditions and health outcomes among these populations are limited. This study investigated the risk factors associated with illnesses among camp-dwelling internally displaced persons (IDPs) in northern Nigeria.Methods A cross-sectional study was conducted in nine camps in 2016. Self-reported data on socio-demography, resource utilization and disease outcomes were collected. Association between health conditions and various factors, including sanitation and healthcare access, was investigated.Results Data from 2253 IDPs showed 81.1% (CI = 79.5–82.7) experienced one or more health conditions; however, over 20% did not access healthcare services. Most common diseases were malaria, fever, typhoid and diarrhoea. Multivariable logistic regression presented as adjusted odds ratios(aOR) and 95% confidence intervals(CIs) showed factors significantly associated with increased likelihood of illnesses included being female (aOR = 1.53;CI = 1.19–1.96), overcrowding (aOR = 1.07;CI = 1.00–1.36), long-term conditions (aOR = 2.72;CI = 1.88–3.94), outdoor defecation (aOR = 2.37;CI = 1.14–4.94) and presence of disease-causing vectors (aOR = 3.71;CI = 1.60–8.60).Conclusion Most diseases in the camps were communicable. Modifiable risk factors such as overcrowding and poor toilet facilities were associated with increased poor health outcomes. This evidence highlights areas of high priority when planning humanitarian public health interventions.