Quasi-one-dimensional Bose–Einstein condensates (BECs) in elongated traps exhibit significant phase fluctuations even at very low temperatures. We present recent experimental results on the dynamic transformation of phase fluctuations into density modulations during time of flight and show the excellent quantitative agreement with the theoretical prediction. In addition we confirm that, under our experimental conditions, in the magnetic trap density modulations are strongly suppressed even when the phase fluctuates. We also discuss our theoretical results on control of the condensate phase by employing a time-dependent perturbation. Our results set important limitations on future applications of BECs in precision atom interferometry and atom optics, but at the same time suggest pathways to overcome these limitations.