If homopolymer repeats of the same nucleotide (e.g. ) are present on the template strand (strand to be sequenced) then multiple introduced nucleotides are incorporated and more hydrogen ions are released in a single cycle. This results in a greater pH change and a proportionally greater electronic signal. This is a limitation of the system in that it is difficult to enumerate long repeats. This limitation is shared by other techniques that detect single nucleotide additions such as pyrosequencing. Signals generated from a high repeat number are difficult to differentiate from repeats of a similar but different number; e.g., homorepeats of length 7 are difficult to differentiate from those of length 8.
Another limitation of this system is the short read length compared to other sequencing methods such as Sanger sequencing or pyrosequencing. Longer read lengths are beneficial for de novo genome assembly. Ion Torrent semiconductor sequencers produce an average read length of approximately 400 nucleotides per read.
The throughput is currently lower than that of other high-throughput sequencing technologies, although the developers hope to change this by increasing the density of the chip.