After heat-shock, HSF1 controls a major cellular transcriptional response involving the activation of early (Hsp70) and late (Hsp25) heat shock gene expression. Here we show that a full response to heat shock (activation of both Hsp70 and Hsp25) depends on the duration of HSF1 activation, which is itself controlled by HDAC6, a unique deacetylase known to bind mono and poly-ubiquitin with high affinity. Based on a comparative analysis of the heat shock response in cells knocked out for HDAC6 or expressing HDAC6 mutants, we show that HDAC6 binding to ubiquitinated proteins controls the duration of HSF1 activation following heat shock. In cells expressing HDAC6 mutated in the ubiquitin-binding domain, the AAA ATPase factor p97/VCP mediates a rapid inactivation of HSF1 precluding the late activation of the Hsp25 gene. In these cells, the knock-down of p97/VCP rescues HSF1 from this rapid inactivation and restores HSP25 expression. Altogether, we present here a new regulatory circuit that adjusts the duration of the heat shock response to the extent of protein ubiquitination after heat shock.