The main objective of this study is to explore the relationships between the phonotactic structure of the Czech stress-group and rhythm of speech. Three most frequent consonantal-vocalic (CV) structures of Czech two-syllable stress-groups were selected for the purpose of this study: CVCV, CVCCV, and CCVCV. In an auditory experiment, which contained the mutual comparison of stress-groups or the comparison of a stress-group and a low-frequency shadow of a stress-group, the respondents established how similar the rhythmic pattern of each couple of stress-groups sounded. The results indicate that the position of a consonantal cluster within the stress-group is the strongest phonotactic factor in perception of the rhythmic similarity. The number of consonants within a consonantal cluster and the presence of a long vowel in both stress-groups are considered weaker factors for perceiving the rhythmic similarity by the respondents. Possibilities for a follow-up research are proposed for the factors that did not reach statistical significance, i.e., the difference in sonority or voicing of consonants.