It is well known that the blood-oxygen level dependent (BOLD) signal measured by functional magnetic resonance imaging (fMRI) is influenced - in addition to neuronal activity - by fluctuations in physiological signals, including arterial CO2. For instance, even spontaneous CO2 fluctuations have been shown to influence the BOLD fMRI signal regionally. Related to this, studies of functional connectivity between different brain regions, performed when the subject is at rest, may be confounded by the effects of physiological noise. Moreover, resting functional connectivity has been shown to vary with respect to time (dynamic functional connectivity), with the sources of this variation not fully understood at present. In this context, in the present paper we examine the relation between dynamic functional connectivity patterns and the properties of the end-tidal CO2 signal (PETCO2) using resting-state fMRI measurements from 12 healthy subjects. The results demonstrate that there exists a modulatory effect of the correlation strength between PETCO2 and the BOLD signal on dynamic resting functional connectivity. The extent to which this effect was observed was found to be strongly dependent on the data analysis methodology.