  In this paper we show how intrinsic alignments can be incorporated
consistently in the formalism of 3d weak lensing. We use two different
descriptions of the intrinsic galaxy ellipticities, the so-called linear and
quadratic model, respectively. For both models we derive the covariance matrix
of the intrinsic alignment signal (II-alignments) and GI-alignments (the cross
correlation of intrinsic and lensing induced ellipticities). Evaluating the
covariance matrices for the linear model numerically and comparing the results
to the cosmic shear signal we find that for a low redshift survey the total
covariance matrix is dominated by the contributions of the II-alignments. For a
Euclid-like survey II-alignments still dominate over GI-alignments but they are
more than one order of magnitude smaller than the lensing signal. The shape of
the ellipticity covariance matrices is quite different in the k-k'-plane for
cosmic shear on the one hand and intrinsic alignments on the other hand. In
comparison to lensing both alignment types tend to be rather elongated along
the diagonal k=k'. Moreover, for high multipoles (l ~ 100) intrinsic alignments
are strongly concentrated along that diagonal.
