Aim: The aim was to compare the performances of the World Health Organization (WHO) and population‐based (PB) references in the screening for hydrocephalus in infants aged <2 years. Methods: We collected 341 longitudinal head circumference (HC) measurements of hydrocephalic infants and 120 181 measurements of 15 145 healthy infants from primary care. The measurements were converted into z‐scores, and a new screening parameter, change in HC standard deviation score (SDS) over time (ΔHC SDS), was calculated. Comparisons were made using receiver operating characteristics analysis and linear mixed models. Results: The mean HC SDSWHO was 3.5 and the mean HC SDSPB was 2.9 in the hydrocephalic infants, and in healthy children, those numbers were 1.0 SDSWHO and 0 SDSPB, respectively. The best screening accuracy was obtained with the PB reference in combination with the ΔHC SDS parameter (AUC 0.89). The accuracy of the WHO standard could be improved to a similar level by customising the screening cut‐offs of HC SDS according to the population and combining screening parameters. Conclusions: Auxology alone was not sufficient for the screening of hydrocephalus. The WHO standard should be validated in the population, and population‐specific cut‐offs for normality defined before its introduction. [ABSTRACT FROM AUTHOR]