Citations published in online supplementary material (OSM) are invisible to search engines used to calculate citation counts, potentially negatively impacting popular performance indices and journal rankings that rely on citation counts for quantification. To quantify the number of citations that are lost in OSM, we conducted a systematic survey of supplementary citation practices in four high-ranking, society-run journals from two geographical locations (Europe and North America). In 2012, 6 of all citations were only included in the OSM and were therefore not included in citation counts. We found a significant increase in the number of references invisible to citation counting services over the last two decades. A solution to this problem is urgently required and could include journal indexing of citations in OSM or the inclusion of all references in the main text.