Unlike the 3.5L in the IS350,GS350..the RX350 doesn't have direct injection.Nor does the ES 350.
I had the same knocking,rapping problem on my '09 RX350 that started at about 20K miles and only in cold weather till engine warmed up..
Dealer service pulled the the noise won't cause any damage to the engine
Where did you get that info? I've had two dealers state (in the process of trying to get them to fix it) that they are direct injected. I've not been able to find any other source, but if you're right I'd like to know where the noise is coming from. Like the others, mine started after 10k or so, and initially it totally went away after a mile or so. Now it is significantly louder (33k miles now) and never totally goes away, and it does it in any temperature, after the car sits for an hour or so. If I knew this would happen (or if the demo car I drove had the noise), I certainly wouldn't have bought it. Likewise, it's loud enough that I'm sure I'll never be able to sell it.
"The 3.5 uses hydraulic valve lifters that continously adjust valve lash. Further if you look at the schematics for the 2GR-FE engine, the pistons are minimally skirted allowing them to rock within the cylinder, this would especially be true at cold start as the pistons have not expanded to match the cylinder sleeve... The tolerance is tight given the fact the pistons are coated to minimize scuffing and also to try and combat cold start knock... It is minimized, but not completely eradicated, therefore Toyota/Lexus will keep telling you it is normal... The noise is not the injectors nor is it the valves, but these are instead simple explainations for simple people."
The 2GR-FSE engine used in the Lexus IS, and GS 350, incorporate Toyota's latest D4-S twin injection fuel system. This system combines direct injection with traditional port injection. Using direct injection and port injection simultaneously facilitates more precise mixing of air and fuel under low and medium load conditions for greater efficiency, while high load conditions dictate the use of direct injection alone for maximum power. The 2GR-FSE engine is rated at 315 PS (232 kW; 311 hp) at 6,400 RPM and 38.4 kg·m (377 N·m; 278 ft·lbf) at 4,800 RPM. The engine's service weight is 174 kg.
2GR-FE engine in the Lexus RX 350
The 2GR-FE is a 3.5 L (3456 cc) version for transverse FWD mounting. Bore remains at 94 mm but stroke is reduced to 83 mm. Reported output varies depending on the vehicle application, but is approximately 266 hp (198 kW) to 275 hp (205 kW) at 6200 rpm with 245 lb·ft (332 N·m) to 257 lb·ft (348 N·m)of torque at 4700 rpm on 87 octane (R+M/2). This version features Toyota's Dual VVT-i, variable valve timing on both the intake and exhaust cams. Valves are driven by roller-follower rocker arms with low friction roller bearings, and a unique, concave cam lobe design to increase valve lift over the traditional shimless lifter type system of the 1GR-FE. This increases overall cylinder head height to accommodate the slightly taller roller rocker system. Moreover, the cylinder head is segmented into 3 parts: valve cover, camshaft sub-assembly housing, and cylinder head sub-assembly. As such, this valvetrain is used across all other GR engines with Dual VVT-i. Its service weight is 163 kg.