Whole Foods is down as much as 6% after hours, to $US52.10.
The retailer reported Q1 earnings of $US0.42 per share, missing expectations for $US0.44 per share.
Q1 comp sales were up 5.4%, missing expectations for a 5.7% rise.
The company also lowered guidance and now sees full-year EPS of $US1.58-$1.65 per share, from $US1.65-$.169 per share.
This was also below expectations for $US1.68 per share.
It expects full-year comp sales up 5.5-6.2%, compared with expectations for 6.2% rise. This is lower than its prior outlook for 5.5-7%.