"Higher yields usually mean large caps do better," it said. "A powerful dollar surge would drive small caps but the greenback already has moved sharply in the past few months and future gains might be much harder to come by."
In the wake of Donald Trump's surprise U.S. election win, the dollar index, which measures the greenback against a basket of currencies, surged to a 14-year high. Larger companies tend to have more overseas earnings, which would be hurt when they are translated back into the greenback.
Trump has since floated the idea of a "border tax" to discourage imports into the U.S. Since larger companies tend to be more likely to import components, equipment or products, tariffs would hurt them more than smaller companies.
Oddly, Citi noted that clients who were pushing back against its call for large caps to outperform, were also pushing back on the bank's call to be overweight financial stocks, which would seem to argue against the smaller-cap index due to its heavier exposure to banks.
4. Citi has gone overweight on media stocks, saying it might be the bank's "most out of consensus view."
"Liking Media stocks generates 'raspberries' as the Street remains deeply concerned about cord-cutting and pricing issues," it said. "However, valuation and earnings revision momentum support the industry group's relative outperformance potential as might M&A activity."
Citi also noted that new technology, such as virtual and augmented reality, could also drive the sector.
—By CNBC.Com's Leslie Shaffer; Follow her on Twitter @LeslieShaffer1
Follow CNBC International on Twitter and Facebook.