In multigate spectral Doppler (MSD) analysis, hundreds of small sample volumes (SVs) aligned along a pulse wave-line can be simultaneously investigated. The so-called spectral profile, reporting the scatterers' velocity distribution in a vessel, is obtained by estimating the frequency content of the echoes detected from each SV. The preferred frequency estimator is the Welch method, which is robust and fast, but requires an observation window (OW) of at least 64 to 128 samples to guarantee adequate spectral resolution. The blood amplitude and phase estimator (BAPES) and the blood iterative adaptive approach (BIAA) are alternative methods which were recently proven to be capable of producing good spectrograms from one SV using shorter OWs. This paper shows that BAPES and BIAA can be successfully applied to MSD estimations. The use of short OWs can be exploited to produce spectral profiles with high temporal resolution and/or to perform simultaneous investigations at multiple sites. Two in vivo examples of application are reported: in the first, the blood velocity distribution during the fast systolic acceleration in a carotid artery is detailed with high temporal resolution; in the second, four spectral profiles are simultaneously detected at different sites of the carotid bifurcation.