Antibiotics and antiseptics have the potential to influence carriage and transmission of meticillin-resistant Staphylococcus aureus (MRSA), although effects are likely to be complex, particularly in a setting where multiple agents are used. Here admission and weekly MRSA screens and daily antibiotic and antiseptic prescribing data from 544 MRSA carriers on an intensive care unit (ICU) are used to determine the effect of these agents on short-term within-host MRSA carriage dynamics. Longitudinal data were analysed using Markov models allowing patients to move between two states: MRSA positive (detectable MRSA carriage) and MRSA negative (no detectable carriage). The effect of concurrent systemic antibiotic and topical chlorhexidine (CHX) on movement between these states was assessed. CHX targeted to MRSA screen carriage sites increased transition from culture positive to negative and there was also weaker evidence that it decreased subsequent transition from negative back to positive. In contrast, there was only weak and inconsistent evidence that any antibiotic influenced transition in either direction. For example, whereas univariate analysis found quinolones to be strongly associated with both increased risk of losing and then reacquiring MRSA carriage over time intervals of one day, no effect was seen with weekly models. Similar studies are required to determine the generalisability of these findings.