Let $ϵ=({ϵ}_n{)}_{n\ge 0}$ be the Thue-Morse sequence, i.e., the sequence defined by the recurrence equations:$${ϵ}_0=1,{ϵ}_{2n}={ϵ}_n,{ϵ}_{2n+1}=1-{ϵ}_n.$$We consider $\left\{\right|{ℰ}_n^p|{\}}_{n\ge 1,p\ge 0}$, the double sequence of Hankel determinants (modulo 2) associated with the Thue-Morse sequence. Together with three other sequences, it obeys a set of sixteen recurrence equations. It is shown to be automatic. Applications are given, namely to combinatorial properties of the Thue-Morse sequence and to the existence of certain Padé approximants of the power series ${\sum }_{n\ge 0}(-1{)}^{{ϵ}_n}{x}^n$.