For integrals involving Gaussians, I've often found it to be more convenient to get integrals via the Expectation value of the MultinormalDistribution.
You can directly apply a convenience function gaussMoment that I posted for that purpose in my answer to How to deal with complicated Gaussian integrals in Mathematica. I'm copying it here:
gaussMoment[fPre_, fExp_, vars_] :=
Module[{coeff, dist, ai, μ, norm},
coeff = CoefficientArrays[fExp, vars, "Symmetric" -> True];
ai = Inverse[2 coeff[[3]]];
μ = -ai.coeff[[2]];
dist = MultinormalDistribution[μ, -ai];
norm = 1/PDF[dist, vars] /. Thread[vars -> μ];
Simplify[
norm Exp[1/2 coeff[[2]].μ + coeff[[1]]] Distribute@
Expectation[fPre, vars \[Distributed] dist]]]
In the first argument, you have to specify the quantity whose expectation value you're interested in, and in the second argument you enter the quadratic polynomial in the exponent of your Gaussian. The integral is done over the variables that you provide as the third argument.
The function doesn't assume that the Gaussian is normalized (it undoes the normalization in Expectation). You could adapt that to your needs if desired.
In your application, I would then use the complex exponentials representing the Fourier basis as the first argument. For the second argument, I just copy the polynomial from your question:
gaussMoment[
Exp[I (kx x + ky y)],
-((x - μ1)^2/σ1^2) - (y - μ2)^2/σ2^2 + (2 ρ (x - μ1) (y - μ2))/(σ1 σ2),
{x, y}]
$$\pi \sqrt{-\frac{\text{$\sigma $1}^2 \text{$\sigma
$2}^2}{\rho ^2-1}} \exp \left(\frac{\text{kx}^2
\text{$\sigma $1}^2+2 \text{kx} \left(\text{ky} \rho
\text{$\sigma $1} \text{$\sigma $2}+2 i \text{$\mu $1}
\left(\rho ^2-1\right)\right)+\text{ky} \left(\text{ky}
\text{$\sigma $2}^2+4 i \text{$\mu $2} \left(\rho
^2-1\right)\right)}{4 \left(\rho ^2-1\right)}\right)$$
As mentioned in the comments to the question, it's a good idea to avoid using Subscript except in typesetting formulas for presentation only, so I made that change.
Subscript[k, x]depends on your variablex. – John Doty Jul 05 '17 at 16:02Subscriptis a nasty things to use. @Sid You probably make many implicit assumptions on what values all the parameters have: sigmas are positive, 0<rho<1 etc. You can helpIntegrateby making your hidden assumptions official with the help of the optionAssumptions. See the documentation on how to use it. You might also consider to useFourierTransform. – Henrik Schumacher Jul 05 '17 at 16:21