Based on plumage traits it is impossible to reliably identify the sex of Water Rail Rallus aquaticus and Spotted Crake Porzana porzana. In order to analyze their sexual size dimorphism we collected morphometric data and, for genetic control, feather pins as DNA source of 71 adult Water Rails and 31 Spotted Crakes during the breeding season 2008–2009. We determined the sex of each individual using PCR based molecular techniques taking into account the length polymorphism of the sex linked CHD1Z allele encountered in Water Rails. The polymorphism of this sex marker may have caused erroneous conclusions in previous studies using different approaches. In the present case, unawareness of the polymorphism would have lead to the misclassification of 50.8% of the individuals, which would result in problems with morphological comparison of the sexes. In general, males of both species were significantly larger than females. However, single measurements partly showed a high overlap of the sexes. Conducting a stepwise discriminant function analysis revealed bill, maximum wing chord and tarsus length as best discriminants for Water Rail. The resultant discriminant function, which allows assigning an individual to one of the sexes with a specific accuracy by its body measurements, correctly classified 98.6%. In Spotted Crakes the analysis included tarsus and wing length into the model and assigned the sex with an accuracy of 100%. The discriminant functions thus represent a simple and cost efficient way to determine the sex of these rallids for field ornithologists.