The breeding system of parasitic protozoa affects the evolution of drug resistance and virulence, and is relevant to disease diagnosis and the development of chemo‐ and immunotherapy. A major group of protozoan parasites, the phylum Apicomplexa, that includes the aetiological agents of malaria, toxoplasmosis and coccidiosis, all have dimorphic sexual stages. The sex ratio (proportion of males produced by parasites) is predicted to depend upon the inbreeding rate, and it has been suggested that sex‐ratio data offer a relatively cheap and easy method for indirectly estimating inbreeding rates. Here, we exploit a new theoretical machinery to show that there are generally valid relationships between f, Wright's coefficient of inbreeding, and sex ratio, z*, the generality being with respect to population structure. To focus the discussion, we concentrate on malaria and show that the previously derived result, f=1–2z*, does not depend on the artificial assumptions about population structure that were previously made. Not only does this justify the use of sex ratio as an indirect measure of f, but also we argue that it may actually be preferable to measure f by measuring sex ratios, rather than by measuring departures from Hardy‐Weinberg genotypic proportions both in malaria and parasites more generally.