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We present near-IR (J and Ks) number counts and colors of galaxies detectedin deep VLT-ISAAC images centered on the Chandra Deep Field and Hubble DeepField-South for a total area of 13.6 arcmin$^2$. The limiting surfacebrightness obtained is Ks$\simeq$22.8 mag/arcsec$^2$ and J$\simeq$24.5(1$\sigma$) on both fields. A d$log$N/dm relation with a slope of $\sim0.34$ inJ and $\sim0.28$ in Ks is found in both fields with no evidence of decline nearthe magnitude limit. The median J-Ks color of galaxies becomes bluer atmagnitudes fainter than Ks$\sim18$, in agreement with the different numbercounts slope observed in the two bands. We find a fraction ($\le5%$ of thetotal sample) of sources with color redder than J-Ks=2.3 at magnitudes Ks$>20$.Most of them appear as isolated sources, possibly elliptical or dusty starburstgalaxies at redshift $z>2$. The comparison of the observed number counts withmodels shows that our J-band and Ks-band counts are consistent with theprediction of a model based on a small amount of merging in a $\Omega=1$cosmology. On the other hand, we fail to reproduce the observed counts if we donot consider merging independently of the parameters defining the universe.Comment: 13 pages, 9 figures, Accepted for publication in A&

Deep near-IR observations of the Chandra Deep Field and of the HDF South