MOTIVATION: The query for the number of reads overlapping a given region is a common step in the analysis of Illumina sequencing data. Sometimes, these queries are not conveniently precomputable. It seems beneficial to make this kind of arbitrary query as fast and convenient as possible. RESULTS: We present Bathometer, a tool that indexes BAM files in a space efficient way, which allows ad hoc queries for the number of reads overlapping any given genomic region to be answered much more quickly than by counting with common tools such as Samtools, while incurring much less disk I/O. AVAILABILITYAND IMPLEMENTATION: Bathometer is implemented in C, licensed under the GNU General Public License version 3+ and freely downloadable from Bitbucket (https://bitbucket.org/ustenzel/bathometer). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.