Ecologists are often required to accurately estimate the number of individuals residing in groups of variable sizes inside opaque shelters. Here, we have used x-rays as a non-destructive solution to this problem in social spiders which reside within collectively built opaque, silken, nest-like retreats. Social spiders are model systems for understanding social organization, collective behaviours and population genetics of inbred populations. Such studies often require an accurate determination of the number of individuals, developmental stages and orientation of individuals within the colony which is difficult without compromising the integrity of their retreat or affecting colony behaviour. We demonstrate the effectiveness of x-rays in accurately estimating colony size in the social spider Stegodyphus sarasinorum Karsch, 1892 (Eresidae). This method can also be applied to evaluate body sizes, developmental stages and individual orientation within the colony. We show that this technique does not alter spider prey-capture behaviour or short-term survival compared to control colonies.