Context : Unveiling the structure of the disks around intermediate-mass pre-main-sequence stars ( Herbig Ae/Be stars ) is essential for our understanding of the star and planet formation process . In particular , models predict that in the innermost AU around the star , the dust disk forms a “ puffed-up ” inner rim , which should result in a strongly asymmetric brightness distribution for disks seen under intermediate inclination . Aims : Our aim is to constrain the sub-AU geometry of the inner disk around the Herbig Ae star R CrA and search for the predicted asymmetries . Methods : Using the VLTI/AMBER long-baseline interferometer , we obtained 24 near-infrared ( H - and K -band ) spectro-interferometric observations on R CrA . Observing with three telescopes in a linear array configuration , each data set samples three equally spaced points in the visibility function , providing direct information about the radial intensity profile . In addition , the observations cover a wide position angle range ( \sim 97 ^ { \circ } ) , also probing the position angle dependence of the source brightness distribution . Results : In the derived visibility function , we detect the signatures of an extended ( Gaussian FWHM \sim 25 mas ) and a compact component ( Gaussian FWHM \sim 5.8 mas ) , with the compact component contributing about two-thirds of the total flux ( both in H - and K -band ) . The brightness distribution is highly asymmetric , as indicated by the strong closure phases ( up to \sim 40 ^ { \circ } ) and the detected position angle dependence of the visibilities and closure phases . To interpret these asymmetries , we employ various geometric as well as physical models , including a binary model , a skewed ring model , and a puffed-up inner rim model with a vertical or curved rim shape . For the binary and vertical rim model , no acceptable fits could be obtained . On the other hand , the skewed ring model and the curved puffed-up inner rim model allow us to simultaneously reproduce the measured visibilities and closure phases . From these models we derive the location of the dust sublimation radius ( \sim 0.4 AU ) , the disk inclination angle ( \sim 35 ^ { \circ } ) , and a north-southern disk orientation ( PA \sim 180-190 ^ { \circ } ) . Our curved puffed-up rim model can reasonably well reproduce the interferometric observables and the SED simultaneously and suggests a luminosity of \sim 29 ~ { } L _ { \sun } and the presence of relatively large ( \gtrsim 1.2 ~ { } \mu m ) Silicate dust grains . Our study also reveals significant deviations between the measured interferometric observables and the employed puffed-up inner rim models , providing important constraints for future refinements of these theoretical models . Perpendicular to the disk , two bow shock-like structures appear in the associated reflection nebula NGC 6729 , suggesting that the detected sub-AU size disk is the driving engine of a large-scale outflow . Conclusions : Detecting , for the first time , strong non-localized asymmetries in the inner regions of a Herbig Ae disk , our study supports the existence of a puffed-up inner rim in YSO disks .