Studies of pitch perception often involve measuring difference limens for complex tones (DLCs) that differ in fundamental frequency (F0). These measures are thought to reflect F0 discrimination and to provide an indirect measure of subjective pitch strength. However, in many situations discrimination may be based on cues other than the pitch or the F0, such as differences in the frequencies of individual components or timbre (brightness). Here, DLCs were measured for harmonic and inharmonic tones under various conditions, including a randomized or fixed lowest harmonic number, with and without feedback. The inharmonic tones were produced by shifting the frequencies of all harmonics upwards by 6.25%, 12.5%, or 25% of F0. It was hypothesized that, if DLCs reflect residue-pitch discrimination, these frequency-shifted tones, which produced a weaker and more ambiguous pitch than would yield larger DLCs than the harmonic tones. However, if DLCs reflect comparisons of component pitches, or timbre, they should not be systematically influenced by frequency shifting. The results showed larger DLCs and more scattered pitch matches for inharmonic than for harmonic complexes, confirming that the inharmonic tones produced a less consistent pitch than the harmonic tones, and consistent with the idea that DLCs reflect F0 pitch discrimination.