Abstract Background Several environmental factors favour the occurrence of acute respiratory disease, which is the main reason for paediatric consultations in our country (Colombia). Tobacco smoke is considered a significant environmental pollutant with a great impact on health. The objective of this study is to estimate the prevalence of cotinine levels measured in urine, in children between 1 to 60 months of age who attended an emergency department with acute respiratory disease. Methods A cross-sectional study was conducted that included children between 1 and 60 months of age with acute respiratory disease who were admitted to the emergency department of the Universidad de La Sabana Clinic between April and July 2016. Results We included 268 patients and 36% were female. Of the total population examined, 33.96% showed positive results for urinary cotinine, of whom 97.8% had values between 10 and 100 ng/ml, which is considered positive for exposure to second-hand smoke. The principal pathology was recurrent wheezing in 43.96% of these cases. Regarding the presence of smokers at home, it is important to mention that in 54.95% of the children with positive urinary cotinine test was no related with smokers at home. And in 45.05% of positive urinary cotinine was evidence of smokers at home, being associated with the positive result P < 0.001 and smoking within the house P = 0.018; smoking when children were present did not have significant P = 0.105. The activities performed after smoking such as hand washing, change of clothes, eating, brushing teeth, did not influence the test result P = 0.627. Conclusions A high prevalence of urinary cotinine was observed, which is associated with the presence of a smoker at home, and this relationship was independent of the activities performed by the smoker after smoking. In addition, a positive test for urinary cotinine was presented in some children without documented exposure to cigarette smoke inside the home, which may be explained by the presence of environmental ...