The rat model can be used to assess ileal protein digestibility rapidly and in first intention, but no standardised method exists. Our objective was to compare methods to assess protein digestibility, depending on collection site (ileum/caecum) and use of a non-absorbable marker. A meal containing either casein, gluten or pea protein and chromium oxide as non-absorbable marker was given to male Wistar rats and the entire digestive content was collected 6 h later. Total chromium recovery was incomplete and variable, depending on protein source. We observed no significant difference in digestibility between the methods for any of the protein sources tested. Although none of the methods tested is optimal, our results suggest that caecal digestibility can be used as a proxy of ileal digestibility in rats without using a non-absorbable marker. This simple method makes it possible to evaluate protein digestibility of new alternative protein sources for human consumption.