Parasitological analyses are often based on invasive methodologies, involving host sacrifice, raising ethical and conservation issues. However, alternative non-invasive approaches may not be always applicable due to the location of the parasite in the host tissue or the quality and reliability of the non-invasive sample per se. In this study, we compare the differences in detectability of intestinal parasites in reptiles using the classical invasive approach (intestine dissection), versus a non-invasive procedure (faecal examination), collected from the same individual host. Our results showed significantly lower detectability of helminths in faeces versus the intestine. Moreover, the number of parasites found in faeces was not explained either by the intensities found in the respective intestine or by the host identity. Several factors may explain the lack of association between the two types of samples, but more importantly, our results highlight the randomness of the presence of parasites in faeces. Even if it is not recommended that comparative studies of either parasite abundance or parasite communities be conducted on the basis of faecal samples, there are other types of studies (i.e. genetic) that can be performed with this source of information, thus avoiding the sacrifice of the host. Due to their wide spectrum of life stages and localization in the host tissue, parasites are challenging candidates for non-invasive sampling and consequently, parasitological methodologies should be carefully selected according to the objective of the study.