We relate a recently introduced non-local geometric invariant of compact strictly pseudoconvex Cauchy-Riemann (CR) manifolds of dimension 3 to various η-invar-iants in CR geometry: on the one hand a renormalized η-invariant appearing when considering a sequence of metrics converging to the CR structure by expanding the size of the Reeb field; on the other hand the η-invariant of the middle degree operator of the contact complex. We then provide explicit computations for a class of examples: transverse circle invariant CR structures on Seifert manifolds. Applications are given to the problem of filling a CR manifold by a complex hyperbolic manifold, and more generally by a Kähler-Einstein or an Einstein metric.1991 Mathematics Subject Classification. 32V05, 32V20, 53C20, 58J28. Key words and phrases. CR manifolds of dimension 3, pseudohermitian structures, eta invariants, contact complex.The second author is supported in part by a Young Researchers aci program of the French Ministry of Research.